Speed
Aerospike faster. Almost any system will be fast with low load or easy access to data, but Aerospike has remained stably fast, optimizing storage capabilities and memory based on SSD. Mongo is fast when used with a lot of RAM, where for caching, but otherwise slow and has poor write performance.
Reliability
Aerospike is very stable, albeit with easier access to data. MongoDB has historically been problematic with data persistence and rollback, but now much better. Because Aerospike has better performance and simpler controls, this leads to less potential scaling problems.
Setup / Configuration
Clustering with Aerospike is much easier to configure, since all nodes are the same, and client drivers automatically handle connections and fault tolerance. MongoDB can be simpler if you are setting up one server, as it runs on other platforms, and you can run it without any configuration.
MongoDB has two main clustering methods, a set of replicas (for accessibility) and scaling (for scalability). We had 5 shards, and each shard had a set of replicas of 3 servers. These are 15 servers for data storage. Then we had 3 configuration servers that supported cluster configuration and had to add 2 arbiter processes after our first major failure in order to cope with the proper elevation of the slave. These are many moving parts, and it is also incredibly difficult to change the layout in the future.
In contrast, Aerospike has taken much less effort, but requires more configuration, most of which cannot be changed after the cluster starts, whereas with MongoDB you can create and modify databases at any time.
Aerospike has the ability to synchronize multiple clusters (which is difficult to configure), so you can have different active data centers that replicate data and receive records, which MongoDB really does not support at all.
Data access
MongoDB has a database / collection / document, where each document is only json. Aerospike has a namespace / set / record, where each record is a set of "bins" with a key, which can then have nested key / value structures. Namespaces are preconfigured and not dynamic, and property names are limited to 14 characters that annoy the job.
Both have secondary indexes, although MongoDB allows you to request anything immediately, while Aerospike requires an index or custom scripts. Both have built-in aggregation structures. Aerospike clients support LUA scripts, but MongoDB supports map reduction and custom javascript functions.
It really depends on the needs of your application, but MongoDB benefits in flexibility, simplified queries, and lower restrictions.
Cost
Both are now open source and free. Both versions have enterprise versions with additional features, but licensing is expensive if you have a lot of data. Aerospike can be cheaper because it requires fewer cars.
Generally
For most scenarios, I would recommend Aerospike. MongoDB's semantics of document storage and flexibility are great, but scaling and maintaining it since a distributed database is painful. Aerospike is fast and reliable and can work with fewer nodes that are easier to scale.
October 2014: Aerospike now offers a dedicated program for qualified startups to get free access to the corporate version.
January 2016: MongoDB released MongoDB Cloud Manager , which is a paid SaaS service that can provide and manage your clusters. This solves a lot of problems with configuring Mongo.
March 2017: Both databases have come a long way. Aerospike now has faster replication and more flexible configuration settings without restarting the entire cluster. MongoDB has a new schema application, improves performance, and even supports connections along with the managed service MongoDB Atlas to remove all scaling problems.
I highly recommend ScyllaDB , which is an open source Cassandra-compatible database with incredible performance, center replication, and no usage restrictions.